v1.7.0

• PresCont() implements the Group Present / Contradicted measure of Goloboff et al. (2003).
• Consistency() also returns the relative homoplasy index of Steell et al. (2023).
• JackLabels() supports multiple trees per iteration (#197)[https://github.com//discussions/197]
• Support single-character matrices in ClusteringConcordance()
• Fix DoNothing(x) to return x (not NULL)
• Remove unused delete_rawdata() due to implementation issues.

v1.6.1

• Handle invariant characters in PolEscapa()
• Handle challenging root positions in PlotCharacter()
• Fix character state colours in app legend
• Tweak documentation

v1.6.0

Improvements

• PlotCharacter() performs ancestral state reconstruction on consensus trees (#179)
• Improve support for constraints in AdditionTree() (#173)
• Support for ordered (additive) characters via TreeTools::Decompose()
• Fix SPR behaviour when move is close to root

App improvements

• Buttons to download consensus trees in app
• Fix display of state labels in app

Housekeeping

• Require R 4.0 (to simplify maintenance)

v1.5.1

• Fix calls to DescendantEdges()

v1.5.0

• MaximumLength() calculates maximum possible length of characters, including with inapplicable tokens
• Consistency() now returns retention index and rescaled consistency index

v1.4.0

New features

• TaxonInfluence() calculates influence of individual taxa on phylogenetic inference

Search improvements

• Default to use equal weighting during ratchet iterations
• Support null constraints in AdditionTree()

App improvements

• Exclude taxa from search in app
• Allow search to continue when loading a new file with different taxon names into the app

Housekeeping

• Update calls to DescendantEdges() for compatibility with 'TreeTools' 1.10.0

v1.3.2

• Use PlotTools::SpectrumLegend() for continuous scales in app
• Restore auto-termination of .t files

v1.3.1

• PlotCharacter() now returns invisibly
• Fix missing character in Wills et al. (2012) dataset
• Search by character text in GUI
• Call C functions using symbols

v1.3.0

New features

• New function LengthAdded() tests which characters contribute to taxon instability, per Pol & Escapa (2009)
• WhenFirstHit() recovers tree search information from tree names
• New vignette on tree space mapping
• Support phylo trees as constraints

GUI improvements

• Support reading characters from Excel spreadsheets
• Allow retention of sub-optimal trees
• Use K-means++ clustering

v1.2.0

• 'shiny' GUI improvements:

  • Export log of tree search commands
  • Export R scripts to reproduce figures
  • Simplify layout
  • Misc bug fixes

• New function QuartetResolution() evaluates how a quartet is resolved in
  each of a list of trees.